[go] AmiGO and annotation qualifiers

[Amelia Ireland]

Hi GO Consortium,

There has been some discussion in the web presence working group about  
the display of NOT annotations and annotations with qualifiers. There  
are two issues; how to display the annotations with qualifiers, and  
how gene product counts for terms with qualifiers should be displayed.  
We'd like to get some feedback from the consortium on these issues  
before releasing the new AmiGO.

Annotations With Qualifiers
===========================

I've made some mock ups of different possible arrangements here:

http://www.ebi.ac.uk/~aji/demo.html
http://www.ebi.ac.uk/~aji/demo2.html
http://www.ebi.ac.uk/~aji/demo3.html

These pages are viewing the GPs annotated to a term (and its  
children), but a similar arrangement will be used to view the terms  
with which a GP is associated.

Which arrangement is the clearest? Things to consider:

- how easy is it to see inconsistent annotations, e.g. the same GP has  
a normal and a NOT annotation?

- is it clear what the qualifier applies to?

- some views (e.g. having the associations with operators/qualifiers  
separated out) require extra calculations to generate and will hence  
be slower

- should the default view contain NOT annotations? Is a GO newbie  
going to understand them?

- is the 'nn gene products' link unambiguous in meaning? Is it helpful  
to know how many GPs there are annotated to a term?


Gene Product Counts
===================

The WPWG discussed generating separate totals for numbers of GPs  
annotated to a term without any qualifier and the no. of GPs annotated  
to a term with each of the other qualifiers (currently the GP count  
for a term *includes* any GPs annotated with 'contributes_to' and  
'colocalizes_with', but *excludes* NOT annotations). How useful would  
this be, and is it intuitive to split the counts up thus, or is it  
confusing (especially for GO newbies)? There is also this to bear in  
mind:

On 24 Jan 2008, at 20:11, Chris Mungall wrote:
> On Jan 24, 2008, at 11:08 AM, Seth Carbon wrote:
>> *) ask chris about splitting the gp count by qualifier (seth)
>
> you mean by contributes_to, the NOT operator etc?
>
> unfortunately it is expensive to pre-compute the gp counts in any  
> way that a single gp can end up in two partitions.
>
> we currently partition by gp db name - no gp can be in > 1. this has  
> the advantage that we can get the correct total by summing the  
> numbers at query time.
>
> however, if we have a partition that does not split gps in this way  
> we can't sum across the partitions, which means we have to pre- 
> compute for all combinations.
>
> This may not be so bad for the qualifiers however, since the  
> qualifiers are relatively rare.
>
> would you really want this for the NOT operator though? remember the  
> semantics are easy to get confused here. Would you want:
>
> all gps that are NOT GPCRs (ie include those that are asserted not- 
> TM receptor in the count) - negation propagates up the graph
>
> all gps that have a NOT annotation to some kind of GPCR - negation  
> propagates as normal



Any feedback would be gratefully received. Thanks!

Amelia / the Web Presence Working Group.

--
Amelia Ireland
GO Editorial Office,
European Bioinformatics Institute, UK.
Carbon neutral driving: http://www.targetneutral.com/TONIC/index.jsp